It turns out Clara is really evil when she takes the Doctor prisoner and flirts with him while the Master returns. She explains she'll take her place at her Master's side, the Doctor warns her of the last time he took a wife but she says she can control the Master as she knows how to manipulate timelords. The master well he's no different, except he can make her queen of the universe.
The Doctor isn’t entirely sure how he came to be lying on the concrete floor of an otherwise nondescript cell, but it’s far from being a new occurrence. He’s not entirely sure why he’s in chains, either, but he figures that whenever he’s usually locked up, Clara is generally with him, so he turns his head to the side in search of her so that they can develop a plan to escape. But he finds nothing on his right, and nothing on his left either, which means she must be locked up somewhere else, and his hearts skip a beat in panic at the thought of what their unknown jailers may be doing to her.
“I’m up here,” comes a cold voice, and he looks up to find Clara stood in the doorway, eyes icy and her mouth set in a cruel smirk. Which would be disturbing in itself, but she’s also unfettered by chains, and seems wholly unmoved by the situation at hand. “You really are such a trusting little fool sometimes.”
“I…” he stammers, and it’s then that he notices the dull ache in his cheek. He reaches up and probes at it experimentally, finding dried blood and broken skin. “What hit me?”
“I did,” she says with unwavering composure, and as he looks up at her he becomes aware of the same dull ache throughout his body. “You were trying to get away, and I couldn’t have that. You bled all over my hand. I let the guards have a little longer with you, for that.”
“Clara, what the hell…” he sighs as the penny drops. “Bonnie, this isn’t funny.”
“Bonnie isn’t here, Doctor,” she pouts in a condescending manner. “Bonnie was the first to die, lest she get any pathetic ideas about taking my place.”
“Don’t be absurd,” Clara snaps, and he feels his stomach lurch as he realises she’s telling the truth. “I don’t get my hands dirty. You being the exception to that rule. I had one of my people do it.”
“Since when did you… since when did you have “people”? And since when were you… evil?”
“Oh, please,” she rolls her eyes. “You truly think Missy would have picked you a good, warm-hearted, loving friend?”
“Yes,” he replies dully. “You are all those things.”
“No,” she snarls, visibly furious at the insinuation. “I pretended to be, and I bided my time. God knows, it was sickening to watch you. God knows, it was vile to have to simper and swoon and hug you and try to make you think I cared. Well, not any more. The time has come for me to take my rightful place at my husband’s side, and for you to stop being a problem.”
“Your… husband?” the Doctor asks, focusing on that one word and feeling a mounting sense of horror. “What husband?”
“Well, my darling husband-to-be,” Clara holds out her hand, and a blood-red jewel set in a silver band glimmers back at him. “You bled all over the damn stone, but I’ve had it cleaned up. At least I know now that you bleed the same colour as all the filthy little humanoids you love so much.”
Her face contorts in fury, and he thinks for one awful moment that she might hit him again. “You will not use that name. You will address me as Mistress.”
“I think Missy might object-”
“Oh, please. Like we could have her flying around and causing problems for us. No. We took care of it.”
“Who the hell is ‘we?’” he snaps, no longer caring about keeping his temper. “You and what army?”
“The Master,” she says in a condescending tone. “My husband-to-be. Goodness, you can be slow.”
“Cl… Mistress,” he says, although the words stick in his throat. “You can’t do that. You can’t marry him. Please. His last wife…”
“Poor unfortunate thing. She went quite mad, didn’t she?”
“He did awful things to her, Clara. Beat her. Messed with her mind. Hurt her in more ways than I can tell you. He’ll do that to you, Cl- Mistress. He’ll hurt you, and he’ll throw you away.”
“He’ll make me queen of the universe,” she told him icily. “And besides, I know how to manipulate you pathetic little Time Lords, remember? Now, be a good boy until the guards take you down to Level Seven.”
“What the hell is Level Seven?”
“Your worst nightmare, Doctor. And your new home, until the end of your days.”